Volume 16, No. 1, January 2024
Introduction
The UK National Electron Diffraction Facility grand opening was held on January 16, 2024. In keeping with the tradition of naming the UK National Crystallographic Service’s instruments after famous female crystallographers, Ada Yonath, Rosalind Franklin, Dorothy Hodgkin and Kathleen Lonsdale, the recently installed XtaLAB Synergy-ED was named Els after Elspeth Garman. This was celebrated at the grand opening with the presentation of a certificate to Elspeth.
Left to right, front row: Simon Coles (Professor of Structural Chemistry and director of the UK NCS and NEDF) Andrew Hector (Head of the School of Chemistry), Mark Benson, Elspeth Garman (Oxford University Emerita) and Hiroyuki Kanda.
Last month marked a momentous occasion as we celebrated the illustrious career of Damian Kucharczyk, the visionary founder of KUMA Diffraction in 1993. After decades of dedicated service, Damian embarked on a well-deserved retirement, leaving an indelible mark on the world of crystallography.
Throughout his remarkable journey, Damian has not only pioneered the field but has also played a pivotal role in shaping the next generation of crystallographers. Countless individuals, both past and present, owe their expertise in the art of crystallography to the innovative instruments he meticulously designed.
Adrian Jones presenting Damian with a retirement gift of a signed group photo of the Rigaku Polska Team.
As Damian transitions into this new chapter of life, we extend our heartfelt wishes for a retirement filled with joy, fulfillment and the satisfaction of a legacy that will endure in the annals of crystallography. Moreover, Damian leaves behind a strong team poised to continue his ground-breaking work, ensuring that the torch of innovation and discovery remains brightly lit in Rigaku. May this well-earned respite be a time of reflection and enjoyment for Damian, who has undeniably enriched the scientific community with his passion and contributions.
This month we highlight the XtaLAB Synergy-S, Mark Del Campo provides the Tip of the Month and Jeanette reviews: Not Just for the Boys: Why We Need More Women in Science
Joe Ferrara and Mark Benson
TOPIQ | High-pressure Crystallography on the Rigaku XtaLAB Synergy-S Diffractometer
In this Webinar, the process of conducting a high-pressure crystallographic experiment on the XtaLAB Synergy-S will be explained and software features in CrysAlisPro relevant to the technique will be covered. High-pressure crystallography provides a tool for researchers to effect changes in the structure of matter and ultimately understand the phenomena such changes can induce.
Wednesday, March 7, 2024 at 09:00 CST
TOPIQ | Pump-multiprobe Photocrystallography on the XtaLAB Synergy-R system
In this Webinar we will describe a new setup, developed in collaboration between Cardiff University and Rigaku, that enables the collection of pump-probe Photocrystallography data down to a time-resolution of 10 ms, producing full, 3D structures at regular time-points to create 3D molecular movies.
Wednesday, January 31, 2024 at 09:00 CST
Presenter: Dr. Lauren Hatcher, Cardiff University
Researcher in the spotlight
Laure Vendier
Laure Vendier (INSA Toulouse engineer, physics engineering option, 1994), obtained her PhD in 1997 in the field of materials for electronics (thesis co-supervised by the INSA Toulouse and the Georgia Institute of Technology in Atlanta).
She was recruited at the CNRS in 1998 for an engineering position at CEMES within the X-ray diffraction department, and joined the LCC in 2003 to take responsibility for the laboratory's XRD platform.
Her main interests are crystallography on small molecules, more specifically the determination of molecular architecture by X-ray diffraction, on sensitive crystals, but also structural studies on powders and nanomaterials by X-ray diffraction. Recently she had the opportunity to train and develop studies under high pressure by XRD on single crystal.
Technique in the spotlight
High-pressure crystallography
High-pressure crystallography has been conducted for many decades now, with the origins of the modern method in approx. the 1970s. The method uses a device called a Diamond Anvil Cell (DAC) to isotropically compress a sample to pressures of up to 100 GPa whilst allowing X-rays to reach and diffract from the sample inside.
The application of pressure can bring structural changes, typically through the modification of intermolecular interactions, which in turn may bring about effects such as phase changes, amorphization, superconductivity, magnetism or polymerization, among others. Understanding these structural changes can lead to an understanding of how to control the effects in a desirable and useful way.
Conducting high-pressure experiments allows researchers to observe 3-dimensional structural changes at pressure, and is a valuable tool in materials science, pharmaceutical research and much more. Modern instrumentation has made high-pressure structural research more accessible than ever before, with advances in software and hardware reducing the entry barrier for new researchers.
If you are interested in this technique and would like to know more, please view our webinar from March 2024.
Product in the spotlight
XtaLAB Synergy-S
With your success utmost in our minds, we have developed the XtaLAB Synergy-S X-ray diffractometer for single crystal X-ray diffraction. Using a combination of leading-edge components and user-inspired software tied together through a highly parallelized architecture, the XtaLAB Synergy-S produces fast, accurate data in an intelligent fashion. The system is based around the PhotonJet-S series of microfocus X-ray sources that optionally incorporate continuously variable divergence slits. These third-generation sources have been designed to maximize X-ray photons at the sample by using a combination of new optics, new longer-life tubes and an improved alignment system. PhotonJet-S sources are available in Cu, Mo or Ag wavelengths in either a single or dual source configuration. The XtaLAB Synergy-S single crystal X-ray diffractometer comes with a kappa goniometer that incorporates fast motor speeds and a unique telescopic two-theta arm to provide total flexibility for your diffraction experiment. The system is also equipped with your choice of HPC hybrid photon counting detectors, the HyPix-6000HE or the large theta coverage detectors: HyPix-Arc 100° or HyPix-Arc 150°.
In some settings, there is a desire to share instrument resources across different research groups. The XtaLAB Synergy-S in a dual-source configuration is the perfect system to be shared between protein crystallographers and chemical crystallographers: a Mo source will give the chemical crystallographers the wavelength necessary to reduce absorption from heavier elements and a Cu source, with optional continuously variable divergence slits, will give the protein crystallographer the functionality necessary to resolve large unit cells.
ACA Summer Course 2024
It is with great pleasure that the organizers of the ACA Summer Course announce the 2024 ACA Summer Course in Chemical Crystallography. The course will be held at Purdue University from June 23-30, 2024. For more details, please check the web page at https://acasummercourse.net/
Applications for the course opened on January 1, 2024.
For international attendees requiring a visa to enter the United States: There have been increasingly long processing periods in recent years to obtain a B1 visa. If you are planning to apply for the course, please contact us as soon as possible.
Should you have any questions, please email info@acasummercourse.net
Organizers
- Allen Oliver (University of Notre Dame), aoliver2@nd.edu
- Matthias Zeller (Purdue University), zeller4@purdue.edu
- Christos Malliakas (Northwestern), c-malliakas@northwestern.edu
- Charlotte Stern (Northwestern), c-stern@northwestern.edu
- Nathaniel Barker (Northwestern), nathaniel.barker@northwestern.edu
Crystallography in the news
November 16, 2023: Researchers from China have synthesized and characterized a triplet Fe compound with a weak Fe-C triple bond that provides some unique synthetic properties.
November 22, 2023: Scientists from Israel and the US used X-ray crystallography and cryo-EM to determine how Gabija proteins assemble into a supramolecular complex that degrades phage DNA in bacteria.
December 7, 2023: Scientists from France and the UK have determined the structure of the glutamate receptor GluD1 with GABA bound. This receptor is present at both excitatory and inhibitory synapses.
January 3, 2024: Scientists from Canada and Spain used NMR and X-ray crystallography to study shuttling of planar guests in a molecular box 22 Å long x 7 Å wide.
January 4, 2024: Researchers from China have synthesized and characterized a stable rhodium-coordinated carbene with a σ0π2 electronic configuration.
January 9, 2024: Scientists from Canada, Germany and Sweden report the use of serial STEM data collection provided high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials.
Tip of the Month: Beam Slit (Divergence) Control
By Mark Del Campo
When using Cu radiation with a Rigaku VHF optic on a XtaLAB Synergy-S, -R, or -DW, diffraction spots can overlap in certain situations. For example, if a crystal is pseudo-merohedrally twinned then the spots from multiple lattices may overlap. Also, if a crystal has one or more large unit cell dimension (>120 Å) then the spots on that long edge may overlap. In both cases, the beam divergence should be reduced using the Beam Slit Control in CrysAlisPro to move the beam slit into the X-ray beam. First, make sure the detector is at the appropriate starting distance based on the unit cell’s largest primitive dimension (i.e., for a Rigaku HyPix detector use a distance in mm equal to the longest cell edge divided by 3). Then, access the Beam Slit Control by a right-mouse-click on the X-RAY button to open a drop-down list, followed by a left-click on Beam slit.
Figure 1. Access the Beam Slit Control.
For a XtaLAB Synergy-S or -R, this opens a Beam Slit Controller interface that shows the current motor position of the slit and the approximate divergence and relative beam intensity. Click on the Set button to open the settings. Then, click and drag the slider to the right to choose a reduction in beam divergence and click OK to move the slit.
Figure 2. The XtaLAB Beam Slit Controller interface.
Figure 3. Beam Slit - Set Values Dialog.
For a XtaLAB Synergy-DW, the DW Beam Slit Controller interface is a little different in appearance, but similar in function. First, click on Init Beam Slit Control to connect to the slit and establish control. Then, click on the right button to change to the scale desired for changing the slit. The options are mR (divergence), % intensity, or mm position of the slit. Then, enter a numerical value in the box that is within the range displayed and click on Set value to move the slit. Finally, click on Exit and disconnect.
Figure 4. The XtaLAB Synergy-DW Beam Slit Controller interface.
Be patient and remember that it may take several rounds of changing the beam divergence followed by a pre-experiment (screening) to establish an appropriate slit setting for a given crystal.
Finally, note that the current slit position of the instrument is always displayed at the top of the image display in CrysAlisPro. And when opening any data set in a data processing instance of CrysAlisPro, the slit setting used for the data can be viewed under the Data Collection executive summary on the right side of the GUI.
Figure 5. The current slit position of the instrument is always displayed at the top of the image display in CrysAlisPro.
Figure 6. The slit setting used for the data can be viewed under the Data Collection executive summary on the right side of the GUI.
Book review
Review: Not Just for the Boys: Why We Need More Women in Science
By Athene Donald
ISBN 9780192893406
Athene Donald’s Not Just for the Boys: Why We Need More Women in Science is a concise but compelling read for anyone and everyone. It’s a book for women who have pursued a career in science, regardless of where they are in that career. It’s also a book for men in the same position. It’s a book for anyone who has a young girl or young woman in their life with an interest in science and math. But it’s also a book for anyone who has a young girl or young woman in their life who doesn’t have an interest in science or math. Indeed, although Donald is writing about the importance of women in science and detailing the historical, present, and future impediments that can keep them from reaching their desired position in their respective fields, much of Donald’s argument can be applied to any field in which men outnumber women.
As a Professor Emerita of Experimental Physics at the University of Cambridge, Donald certainly has her own breadth of experience navigating science and academia as a woman. And while she does draw on that experience, much of Not Just for the Boys includes numerous anecdotes and personal stories from women across scientific disciplines, as well as explanations of research findings from studies designed to determine if gender gaps really do exist in the sciences, both at the professional and student level (spoiler alert: they do).
Donald begins with a chapter entitled “What’s the Problem?” in which she outlines and addresses the issues at hand—namely, after decades of initiatives to increase the number of women in science and the fact that the population of the world is roughly 50% women, women do not account for 50% of scientists. She then proceeds to delve into the issue as deeply as she can in a book of a little over 200 pages, starting with how scientists are perceived in society (mostly as men) and how that impacts young women’s perceptions of what they can be. She also digs into what can keep young women from pursuing roles in scientific careers even if they have a proven interest, and what obstacles women can face once they’ve already made their career in the sciences. At the end of the day, it’s still a man’s world, and science is no exception.
Donald argues that science, like any field, benefits from the diversity of those pursuing it. She acknowledges that, as a white woman, she still garners certain privileges not afforded to colleagues of color, particularly women of color. But Donald also acknowledges that as a white woman, she is not the right person to be writing a book about intersectionality in the sciences. While Donald’s book will certainly resonate for any woman in the sciences, if you’re looking for a read about women of color in the sciences, Jasmine Brown’s Twice as Hard is an excellent choice.
Review by Jeanette S. Ferrara, MFA
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